The role of ethics in experimental marine biology and ecology

Although most countries have ethical guidelines for research involving human subjects and other sentient animals, the ethical issues associated with field research have received little attention. Most experimental marine biologists and ecologists operate without ethical guidelines or scrutiny, despite intermittent community concern about their activities. We offer suggestions on how marine biologists and ecologists can protect the future of research involving the field collection and experimental manipulation of organisms by developing mechanisms to address community concerns that such research is ethically responsible. We urge experimental marine biologists and ecologists to take pre-emptive initiatives by encouraging: (1) institutional animal ethics committees to broaden their terms of reference to include environmental ethics; (2) scientific societies to develop codes of ethics to guide the environmental research conducted by their members; (3) editorial boards of journals to require the research they publish to conform to an appropriate code of ethics, and (4) management agencies that issue permits for field research to establish an ethics committee to advise them on the ethical issues raised by specific research proposals. We conclude that the resultant administrative burden on scientists would be low but that the penalties of operating without such protection can be high.     

Marine speciation on a small planet

The scale of population structure in many marine species is on the order of thousands to tens of thousands of kilometers. How does speciation take place in oceans that are only about this same size? Recent results suggest an important role for transient isolation, gamete ecology and molecular evolution at gamete recognition loci. These factors have long been appreciated by plant biologists, and are likely to be a fruitful area of research for marine biologists as well.     

Beyond Paradise—Meeting the Challenges in Tropical Biology in the 21st Century

Tropical ecosystems support a diversity of species and ecological processes that are unparalleled anywhere else on Earth. Despite their tremendous social and scientific importance, tropical ecosystems are rapidly disappearing. To usher tropical ecosystems and the human communities dependent upon them through the environmental transformations of the 21st century, tropical biologists must provide critical knowledge in three areas: 1) the structure and function of tropical ecosystems; 2) the nature and magnitude of anthropogenic effects on tropical ecosystems; and 3) the socio‐economic drivers of these anthropogenic effects. To develop effective strategies for conservation, restoration, and sustainable management of tropical ecosystems, scientific perspectives must be integrated with social necessities. A new set of principles built on a framework for pursuing relevant tropical biological research will facilitate interdisciplinary approaches, integrate biological knowledge with the social sciences, and link science with policy. We propose four broad recommendations for immediate action in tropical biology and conservation that are fundamental to all biological and social disciplines in the tropics: 1) assemble and disseminate information on life's diversity in the tropics; 2) enhance tropical field stations and build a worldwide network to link them with tropical field biologists at their field sites; 3) bring the field of tropical biology to the tropics by strengthening institutions in tropical countries through novel partnerships between tropical and temperate zone institutions and scientists; and 4) create concrete mechanisms to increase interactions between tropical biologists, social scientists, and policy makers.     

Extending Standards for Genomics and Metagenomics Data: A Research Coordination Network for the Genomic Standards Consortium (RCN4GSC)

Through a newly established Research Coordination Network for the Genomic Standards Consortium (RCN4GSC), the GSC will continue its leadership in establishing and integrating genomic standards through community-based efforts. These efforts, undertaken in the context of genomic and metagenomic research aim to ensure the electronic capture of all genomic data and to facilitate the achievement of a community consensus around collecting and managing relevant contextual information connected to the sequence data. The GSC operates as an open, inclusive organization, welcoming inspired biologists with a commitment to community service. Within the collaborative framework of the ongoing, international activities of the GSC, the RCN will expand the range of research domains engaged in these standardization efforts and sustain scientific networking to encourage active participation by the broader community. The RCN4GSC, funded for five years by the US National Science Foundation, will primarily support outcome-focused working meetings and the exchange of early-career scientists between GSC research groups in order to advance key standards contributions such as GCDML. Focusing on the timely delivery of the extant GSC core projects, the RCN will also extend the pioneering efforts of the GSC to engage researchers active in developing ecological, environmental and biodiversity data standards. As the initial goals of the GSC are increasingly achieved, promoting the comprehensive use of effective standards will be essential to ensure the effective use of sequence and associated data, to provide access for all biologists to all of the information, and to create interdisciplinary opportunities for discovery. The RCN will facilitate these implementation activities through participation in major scientific conferences and presentations on scientific advances enabled by community usage of genomic standards.     

New paradigms for supporting the resilience of marine ecosystems

Resource managers and scientists from disparate disciplines are rising to the challenge of understanding and moderating human impacts on marine ecosystems. Traditional barriers to communication between marine ecologists, fisheries biologists, social scientists and economists are beginning to break down, and the distinction between applied and basic research is fading. These ongoing trends arise, in part, from an increasing awareness of the profound influence of people on the functioning of all marine ecosystems, an increased focus on spatial and temporal scale, and a renewed assessment of the role of biodiversity in the sustainability of ecosystem goods and services upon which human societies depend. Here, we highlight the emergence of a complex systems approach for sustaining and repairing marine ecosystems, linking ecological resilience to governance structures, economics and society.     

A Difficult Time with the Permit Process

In the 1970s, new forms of public scrutiny were applied to the research methods of field biologists in the United States, particularly those studying endangered species and marine mammals. This paper shows how such scrutiny affected researchers’ choice of research methods through an analysis of a key moment in a decade-long controversy over the conservation of bowhead whales. In 1978, researchers at the Naval Arctic Research Laboratory received funding from the Bureau of Land Management to radio-tag bowhead whales. Although this promising but still largely untested technique might have answered one of the central scientific questions in the controversy, it ultimately went unused. Technical considerations played a role in the decision not to use the technique, but the most important factor was scientists’ concerns about potential backlash from Iñupiat whalers and animal protectionists. The same forces that had made marine mammalogists more influential than ever and that had put into their hands the resources necessary to develop more effective research techniques also placed serious constraints on where, when, and how they could do their research.     

Piezophilic adaptation: a genomic point of view

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. As oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. One of the key environment variables that influences the life and evolution of deep-sea organisms is high pressure. This extreme widespread condition requires specific adaptations, the nature of which remains largely unknown. Recent advances in genomic approaches, such as in sequencing technologies and global expression profiling, are rapidly increasing the data available to understand microbial evolution, biochemistry, physiology and diversity. This review summarises the analysis of the results published so far about microbial high pressure adaptation from a genomic point of view. Understanding high pressure adaptation mechanisms is not just a scientific exercise but has important biotechnological implications. For example, hydrostatic pressure is a reality for food science and technology, both for food preparation and preservation. An understanding of the effects of pressure on biomolecules will expand its use in the medical, industrial and biotechnological fields.     

Iles Eparses (SW Indian Ocean) as reference ecosystems for environmental research

TAAF ensures since 2007 the management of 5 small tropical islands lying in the southwestern Indian Ocean: the Iles Eparses. These islands share an exceptional natural heritage including many marine and terrestrial endemic species. At a regional scale the Iles Eparses are some of the most pristine ecosystems, largely preserved from anthropogenic impacts due to their geographical isolation and a historically very limited human occupation. In this context, TAAF wished that Iles Eparses become unique natural laboratories for earth scientists and environmental process observation – like climate change impacts - but also sustainable biodiversity sanctuaries for which the scientific community should provide baseline ecological data to inform on appropriate conservation tools. An inter-agency research consortium emerged in 2009 to meet this commitment for the Iles Eparses. This program was intended to set a science framework in accordance with France' objectives for Research and Conservation. It enabled between 2009 and 2014 the implementation of 18 cross-disciplinary research projects ranging from geology to ecology and represented by the variety of the proposed articles in this special issue. Altogether research projects have dramatically increased knowledge on the Iles Eparses' ecosystems and have provided the first overview of their diversity, their functions and their dynamics and its determinants. In particular applied research efforts have supplied a significant amount of ecological evidence that is now available to develop optimal conservation strategy to ensure the Iles Eparses' long-term biodiversity value. These findings point out that the continuation of research activity in the Iles Eparses should be considered a priority.     

Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus)

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation < 1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.     

Adaptation and the Importance of Local Culture: Creating a Research School at the Scripps Institution of Oceanography

In the 1930s and 1940s a researchschool developed among scientists at theScripps Institution of Oceanography in LaJolla, California. Although that was due inlarge part to Harald U. Sverdrup, a prominentNorwegian oceanographer who served as Scrippsdirector from 1936 to 1948, this paperemphasizes the adaptive, evolving character ofthat research school. Conditions at Scrippsprior to Sverdrup's arrival influenced hisefforts in successfully organizing a group ofscientists. Once at Scripps Sverdrup proved tobe an able leader, but he also had to adapt tothe local scientific culture. Trained in atradition that emphasized the study of physics,chemistry and meteorology, Sverdrup's emphasison dynamical oceanography had a powerful impacton his new colleagues. But in the process hisunderstanding of oceanography also evolved. Hebecame more fully aware of the importance ofbiological and geological investigations, andit was only through close interaction with andreliance on a diverse group of scientists thatthere emerged an ecological understanding ofthe oceans that became a hallmark of Scrippsoceanography. Emphasizing the importance ofadaptation and interaction, and the work ofother scientists in addition to a group leader,this paper offers new insights into theformation of research schools.     

The New Paradox in Marine Scientific Research: Regulating the Potential Environmental Impacts of Conducting Ocean Science

Concerns about the negative effects of marine scientific research are in clear juxtaposition to the beneficial role that scientific knowledge plays in enhancing the understanding of the oceans and protecting the marine environment. This presents a regulatory paradox that is examined in this article in light of the legal framework in the 1982 United Nations Convention on the Law of the Sea. The article traces how these general principles in the Convention are elaborated in soft law instruments for the promotion of environmentally sustainable research practices. It also looks at an example of state practice in this area by examining regulatory measures instituted in the Canadian Endeavour Hydrothermal Vent Marine Protected Area.     

The new tools revolutionizing Vibrio science

As microbiologists we live in exciting times. A variety of technical and conceptual developments, particularly in the last decade have revolutionized the field of microbiology, redrawing the landscape, and entirely redefining what is possible. Perhaps this paradigm shift is no more apparent than in the study of vibrios. The family Vibrionaceae are almost unique as a group of bacteria to study in microbiology: they are genomically, phylogenetically and functionally diverse yet a distinct group of environmental bacteria encompassing important human and animal pathogens as well as non-pathogenic species such as ecologically critical symbionts. Sensitive to physiochemical stimuli, they are among the fasting replicating bacteria studied, capable of responding almost immediately to favourable environmental conditions such as those afforded by climate warming. Characterized by an unusual double chromosome and frequently carrying numerous cryptic plasmids – their genomes are often pockmarked with insertion elements, transposons, prophages and integrases – paying testament to past genomic promiscuity. With a strong affinity for environmental niches in freshwater and marine systems, they are among the most numerous bacteria present in our oceans, coasts and freshwater environments. As such they offer something for almost anyone interested in microbiology and represent an excellent example of field of microbiology that has benefitted hugely by advances across a gamut of disciplines – not just microbiological – but encompassing genomics, genetics, oceanography, ecological, earth observations sciences and data visualization, among others. We will briefly outline some of the most exciting, innovative and translational scientific advances that are currently being applied to these ecologically, environmentally and clinically important bacteria.     

基于近海健康评价现有体系的我国普适海洋健康评价“双核”新框架的构建

海洋生态环境保持健康状态是人类可持续开发利用海洋资源环境的基础,而近海海洋生态环境的健康状况综合评价可为海洋生态环境良性发展以及社会经济决策提供科学依据。首先对国际上3种代表性的海洋环境健康综合评价方法的应用特点进行了对比分析,并归纳了我国海洋生态环境健康评价的状况,在此基础上,以指标体系法重构了一个双核结构的综合评价框架,其中内核评价以海洋生态系统的自身状态为主,外核评价则主要反映海洋之于人类经济社会的贡献,以期能够科学、准确、全面的评价我国近海海洋环境健康状况。     

2015年海南省生态学会青年科技工作者学术研讨会述评

为探讨生态学最新前沿和进展,加强青年生态学科技工作者之间的交流与合作。 2015年11月28-30日在海南大学举行了以“加强合作研究,服务地方发展”为主题的2015年海南省生态学会青年科技工作者学术研讨会,有22位生态学领域的科技工作者做了大会报告,内容涵盖了森林生态系统固碳功能、热带云雾林群落生态学、动物寄生行为生态、道路生态、热带植物的分布与进化、生物多样性、生态恢复、环境生态承载力、生态友好行社区建设模式、生态系统生理学、海洋生态风险评估等。     

Marine molecular biology: an emerging field of biological sciences

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.     

Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010

This report summarizes the proceedings of the 2(nd) Annual Argonne Soils Workshop held at Argonne National Laboratory October 6-8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was "designing ecologically meaningful soil metagenomics research", which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools.     

Cell biology, chemogenomics and chemoproteomics

The scientific techniques used in molecular biological research and drug discovery have changed dramatically over the past 10 years due to the influence of genomics, proteomics and bioinformatics. Furthermore, genomics and functional genomics are now merging into a new scientific approach called chemogenomics. Advancements in the study of molecular cell biology are dependent upon "omics" researchers realizing the importance of and using the experimental tools currently available to cell biologists. For example, novel microscopic techniques utilizing advanced computer imaging allow for the examination of live specimens in a fourth dimension, viz., time. Yet, molecular biologists have not taken full advantage of these and other traditional and novel cell biology techniques for the further advancement of genomic and proteomic-oriented research. The application of traditional and novel cellular biological techniques will enhance the science of genomics. The authors hypothesize that a stronger interdisciplinary approach must be taken between cell biology (and its closely related fields) and genomics, proteomics and bio-chemoinformatics. Since there is a lot of confusion regarding many of the "omics" definitions, this article also clarifies some of the basic terminology used in genomics, and related fields. It also reviews the current status and future potential of chemogenomics and its relationship to cell biology. The authors also discuss and expand upon the differences between chemogenomics and the relatively new term--chemoproteomics. We conclude that the advances in cell biology methods and approaches and their adoption by "omics" researchers will allow scientists to maximize our knowledge about life.     

Overexploiting marine ecosystem engineers: potential consequences for biodiversity

Overfishing is a major environmental problem in the oceans. In addition to the direct loss of the exploited species, the very act of fishing, particularly with mobile bottom gear, destroys habitat and ultimately results in the loss of biodiversity. Furthermore, overfishing can create trophic cascades in marine communities that cause similar declines in species richness. These effects are compounded by indirect effects on habitat that occur through removal of ecological or ecosystem engineers. Mass removal of species that restructure the architecture of habitat and thus increase its complexity or influence the biogeochemistry of sediments could have devastating effects on local biodiversity and important water–sediment processes. The possible overexploitation of engineering species requires more attention because the consequences extend beyond their own decline to affect the rest of the ecosystem. This is particularly problematic in the deep ocean, where oil and gas exploration and fishing pressure are likely to increase.     

Biological control of marine invasive species: cautionary tales and land-based lessons

Biological control (biocontrol) has successfully regulated pest populations in terrestrial agroecosystems, but it has also caused negative unintended consequences for native species. Marine biologists and resource managers have recently published a growing number of proposals to include biocontrol in integrated pest management programs in oceans, seas and estuaries. Here, I review six ecologically and taxonomically diverse case studies of marine biocontrol programs at various stages of planning and implementation. Proposals include viral or microbial control of harmful algal blooms, predatory control of the ctenophore Mnemiopsis leidyi in the Black Sea, parasitic regulation of the European green crab Carcinus maenas, castration by ciliates of the seastar Asterias amurensis in Australia, herbivory of the toxic green alga Caulerpa taxifolia in the Mediterranean by sacoglossan sea slugs, and insect biocontrol by the planthopper Prokelesia marginata to ameliorate ecological impacts of the saltmarsh cordgrass Spartina alterniflora. Where data exist, I evaluate these examples in terms of lessons marine invasion biologists can glean from the rich history of terrestrial biocontrol, and explicitly contrast agroecosystems with invaded marine habitats. Host specificity cannot be guaranteed in the marine biocontrol proposals examined. Feasible alternatives to classical biocontrol in the marine realm should be emphasized, including more investment in invasion prevention tools, early detection and eradication while invasions are small, and increased attention to native natural enemies to control exotic pests. Biocontrol in marine habitats is risky: it poses many more uncertainties and has a much sparser history than its counterpart on land.